Projects in Awesome Lists tagged with single-cell

https://github.com/bowang-lab/scgpt

foundation-model gpt single-cell

Last synced: 14 May 2025

https://github.com/theislab/single-cell-best-practices

https://www.sc-best-practices.org

book rna-seq single-cell tutorial

Last synced: 11 Oct 2025

https://github.com/bowang-lab/scGPT

foundation-model gpt single-cell

Last synced: 01 May 2025

https://github.com/aipoch/medical-research-skills

Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.

academic-writing agent-skills ai bioinformatics biology cancer-genomics clinical-research computational-biology data-analysis data-visualization differential-expression genomics medical medical-research protocol-design rna-seq-data science scrna-seq-data single-cell spatial-transcriptomics

Last synced: 07 Jun 2026

https://github.com/COMBINE-lab/salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

10x bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq sailfish salmon scrna-seq selective-alignment single-cell single-cell-rna-seq transcriptome

Last synced: 11 May 2025

https://github.com/mdozmorov/scRNA-seq_notes

A list of scRNA-seq analysis tools

scrna-seq single-cell

Last synced: 04 May 2025

https://github.com/mdozmorov/scrna-seq_notes

A list of scRNA-seq analysis tools

scrna-seq single-cell

Last synced: 15 May 2025

https://github.com/cafferychen777/mllmcelltype

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

bioinformatics cell-type-annotation computational-biology consensus-algorithm large-language-models llm scanpy scrna scrnaseq-analysis seurat single-cell

Last synced: 08 Feb 2026

https://github.com/aertslab/pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

gene-regulatory-network single-cell transcription-factors transcriptomics

Last synced: 08 Apr 2026

https://github.com/Starlitnightly/omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

bioinformatics bulk-rna-seq omics single-cell

Last synced: 16 Mar 2025

https://github.com/KrishnaswamyLab/PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

data-visualization dimensionality-reduction manifold-learning single-cell unsupervised-learning

Last synced: 08 Apr 2025

https://github.com/gao-lab/glue

Graph-linked unified embedding for single-cell multi-omics data integration

bioinformatics deep-learning single-cell single-cell-multiomics

Last synced: 14 Jan 2026

https://github.com/agitter/single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

bioinformatics pseudotime-algorithms rna-seq single-cell

Last synced: 15 Feb 2026

https://github.com/welch-lab/liger

R package for integrating and analyzing multiple single-cell datasets

nonnegative-matrix-factorization r single-cell

Last synced: 05 Apr 2026

https://github.com/gao-lab/GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

bioinformatics deep-learning single-cell single-cell-multiomics

Last synced: 15 Jul 2025

https://github.com/stuart-lab/signac

R toolkit for the analysis of single-cell chromatin data

atac bioinformatics single-cell

Last synced: 22 Feb 2026

https://github.com/milaboratory/mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

10x antibody bioinformatics immunology rep-seq rna-seq sequencing single-cell t-cell t-cell-receptor

Last synced: 20 Jan 2026

https://github.com/theislab/scarches

Reference mapping for single-cell genomics

batch-correction data-integration deep-learning human-cell-atlas multimodal-deep-learning multiomics rna-seq-analysis scrna-seq single-cell single-cell-genomics

Last synced: 11 Oct 2025

https://github.com/scverse/rapids-singlecell

rapids-singlecell: GPU-accelerated framework for scRNA analysis

anndata bioinformatics gpu scverse single-cell

Last synced: 01 Apr 2026

https://github.com/luntergroup/octopus

Bayesian haplotype-based mutation calling

bioinformatics de-novo-mutation genomics haplotypes phasing single-cell somatic-variants variant-calling variants

Last synced: 14 Jan 2026

https://github.com/theislab/scgen

Single cell perturbation prediction

bioinformatics deep-learning generative-model scrna-seq single-cell single-cell-genomics transcriptomics

Last synced: 11 Oct 2025

https://github.com/scverse/pertpy

Single-cell perturbation analysis

perturbation scverse single-cell

Last synced: 02 Apr 2026

https://github.com/sdparekh/zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

barcodes dge expression fastq pipeline rna-seq rnaseq single-cell umi

Last synced: 09 Apr 2025

https://github.com/samuel-marsh/sccustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization

Last synced: 15 May 2025

https://github.com/kharchenkolab/pagoda2

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

scrna-seq single-cell single-cell-rna-seq transcriptomics

Last synced: 21 Feb 2026

https://github.com/isee/isee

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 20 Oct 2025

https://github.com/iSEE/iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Last synced: 30 Jul 2025

https://github.com/scverse/rapids_singlecell

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

anndata bioinformatics gpu scverse single-cell

Last synced: 27 Feb 2026

https://github.com/vitessce/vitessce

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

data-visualization gehlenborglab hidivelab hubmap imaging kharchenkolab single-cell vitessce zarr

Last synced: 14 Apr 2025

https://github.com/dtm2451/dittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

color-blind color-blindness rna-seq single-cell single-cell-rna-seq visualization

Last synced: 28 Apr 2025

https://github.com/enblacar/scpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.

data-visualization ggplot2 publication-quality-plots r rstats seurat single-cell single-cell-genomics single-cell-rna-seq visualization

Last synced: 24 Jun 2025

https://github.com/dtm2451/dittoseq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

color-blind color-blindness rna-seq single-cell single-cell-rna-seq visualization

Last synced: 28 Jun 2025

https://github.com/saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics

Last synced: 15 May 2025

https://github.com/dtm2451/DittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

color-blind color-blindness rna-seq single-cell single-cell-rna-seq visualization

Last synced: 08 Apr 2025

https://github.com/theislab/moscot

Multi-omic single-cell optimal transport tools

optimal-transport single-cell

Last synced: 11 Oct 2025

https://github.com/hms-dbmi/scde

R package for analyzing single-cell RNA-seq data

analysis bioinformatics heterogenity ngs r single-cell transcriptomics

Last synced: 05 Jun 2026

https://github.com/sanderlab/scPerturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

cite-seq database perturbation python r scatac-seq science scrna-seq single-cell statistics

Last synced: 09 May 2026

https://github.com/COMBINE-lab/alevin-fry

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

10x quantification rna-seq rust single-cell single-cell-rna-seq transcriptomics

Last synced: 28 Apr 2025

https://github.com/hemberg-lab/scrna.seq.datasets

Collection of public scRNA-Seq datasets used by our group

aws dataset docker jenkins mkdocs openstack s3-storage single-cell

Last synced: 20 Aug 2025

https://github.com/stemangiola/tidyseurat

Seurat meets tidyverse. The best of both worlds.

dplyr ggplot2 normalization pca purrr sct seurat single-cell single-cell-rna-seq tibble tidyr tidyverse transcripts tsne umap

Last synced: 21 Feb 2026

https://github.com/cangermueller/deepcpg

Deep neural networks for predicting CpG methylation

deep-neural-networks deeplearning epigenetics methylation single-cell

Last synced: 14 Jan 2026

https://github.com/saeyslab/multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

cell-cell-communication cell-cell-interaction differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology

Last synced: 26 Feb 2026

https://github.com/theislab/chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

disentanglement drug-discovery genomics perturbation single-cell transfer-learning

Last synced: 09 May 2026

https://github.com/celvoxes/cellama

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

celltype large-language-models llm rna-seq scanpy seurat single-cell

Last synced: 07 May 2025

https://github.com/saezlab/liana-py

LIANA+: an all-in-one framework for cell-cell communication

cell-cell-communication ligand-receptor python single-cell single-cell-rna-seq spatial spatialomics

Last synced: 05 Apr 2025

https://github.com/juexinwang/scGNN

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

graph-neural-network scrna-seq-analysis single-cell

Last synced: 21 Jul 2025

https://github.com/satijalab/seurat-data

Dataset distribution for Seurat

datasets single-cell single-cell-genomics

Last synced: 05 Apr 2025

https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

bioconductor jupyter rpy2 scanpy single-cell

Last synced: 16 May 2025

https://github.com/kanaverse/kana

Single cell analysis in the browser

bioinformatics cite-seq exploratory-data-analysis interactive-analysis interactive-visualizations rna-seq single-cell webassembly

Last synced: 07 May 2025

https://github.com/plger/scdblfinder

Methods for detecting doublets in single-cell sequencing data

doublets single-cell

Last synced: 05 Apr 2025

https://github.com/timoast/sinto

Tools for single-cell data processing

bioinformatics single-cell

Last synced: 13 Oct 2025

https://github.com/theislab/chemcpa

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

disentanglement drug-discovery genomics perturbation single-cell transfer-learning

Last synced: 11 Oct 2025

https://github.com/sanderlab/scperturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

cite-seq database perturbation python r scatac-seq science scrna-seq single-cell statistics

Last synced: 09 Apr 2025

https://github.com/single-cell-data/tiledb-soma

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

single-cell single-cell-genomics tiledb tiledb-api tiledb-soma

Last synced: 05 Mar 2026

https://github.com/pachterlab/kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

bustools kallisto rna-seq single-cell

Last synced: 03 Nov 2025

https://github.com/mangiolalaboratory/sccomp

Mixed-effect model to test differences in cell type proportions from single-cell data, in R

batch-correction bayesian composition cytof differential-proportion microbiome multilevel proportions r-package random-effects single-cell unwanted-variation

Last synced: 20 Oct 2025

https://github.com/ZJUFanLab/scDeepSort

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

annotation cell-type-classification deep-learning gnn graph-neural-network reference-free scrna-seq single-cell transcriptomics

Last synced: 21 Jul 2025

https://github.com/bvieth/powsimR

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

experimental-design gene-expression power power-analysis r rna-seq simulation simulation-framework single-cell

Last synced: 11 May 2025

https://bvieth.github.io/powsimR/

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

experimental-design gene-expression power power-analysis r rna-seq simulation simulation-framework single-cell

Last synced: 08 Apr 2025

https://gregoryschwartz.github.io/too-many-cells/

Cluster single cells and analyze cell clade relationships with colorful visualizations.

bioinformatics-algorithms bioinformatics-pipeline single-cell single-cell-analysis single-cell-rna-seq visualization

Last synced: 09 Apr 2025

https://github.com/davisidarta/topometry

Systematically learn and evaluate manifolds from high-dimensional data

clustering data-science data-visualization dimensionality-reduction graph graph-layout hypothesis-generation laplace-beltrami machine-learning manifold-learning scikit-learn single-cell visualization

Last synced: 20 Aug 2025

https://github.com/lilab-bcb/cirrocumulus

Bring your single-cell data to life

10x anndata bioinformatics data-visualization scanpy scrna-seq seurat single-cell smartseq2 spatial transcriptomics visualization webgl

Last synced: 02 Apr 2026

https://github.com/MangiolaLaboratory/sccomp

Testing differences in cell type proportions from single-cell data.

batch-correction bayesian composition cytof differential-proportion microbiome multilevel proportions r-package random-effects single-cell unwanted-variation

Last synced: 07 Oct 2025

https://github.com/scvae/scvae

Deep learning for single-cell transcript counts

deep-learning genomics machine-learning single-cell

Last synced: 09 Apr 2026

https://github.com/catavallejos/BASiCS

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

bayesian bioconductor-package gene-expression r rcpp rcpparmadillo scrna-seq single-cell

Last synced: 08 Apr 2025

https://github.com/catavallejos/basics

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

bayesian bioconductor-package gene-expression r rcpp rcpparmadillo scrna-seq single-cell

Last synced: 06 Apr 2025

https://github.com/gao-lab/Cell_BLAST

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

bioinformatics deep-learning single-cell single-cell-rna-seq

Last synced: 08 Apr 2025

https://github.com/neurogenomics/magma_celltyping

Find causal cell-types underlying complex trait genetics

genomics gwas magma single-cell single-cell-omics snps statistical-genetics

Last synced: 16 Oct 2025

https://github.com/vandijklab/cell2sentence-ft

Cell2Sentence turns scRNA-seq data into text for LLM training.

bioinformatics scrna-seq scrna-seq-data single-cell

Last synced: 16 Jan 2026

https://github.com/Hoohm/CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay

10x citeseq dropseq single-cell

Last synced: 09 Apr 2025

https://github.com/teichlab/genes2genes

Aligning gene expression trajectories of single-cell reference and query systems

bayesian-inference dynamic-programming human-cell-atlas minimum-message-length pseudotime-trajectory python scrna-seq single-cell trajectory-alignment

Last synced: 29 May 2026

https://github.com/sib-swiss/single-cell-training

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

bioinformatics course rna-seq single-cell teaching tutorial

Last synced: 05 Apr 2025

https://github.com/dynverse/dyngen

Simulating single-cell data using gene regulatory networks 📠

benchmarking single-cell single-cell-analysis single-cell-omics

Last synced: 17 Mar 2026

https://github.com/calico/scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

adversarial-training rna-seq semi-supervised single-cell single-cell-genomics

Last synced: 16 Jan 2026

https://github.com/dynverse/dynverse

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

benchmarking scrna-seq single-cell single-cell-omics single-cell-rna-seq trajectory-inference-methods

Last synced: 24 Dec 2025

https://github.com/ZJUFanLab/SpaTalk

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data

cell-cell-communication cell-cell-interaction graph-network knowledge-graph ligand-receptor-interaction single-cell spatial-data-analysis spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 30 Apr 2025

https://github.com/aertslab/SCope

Fast visualization tool for large-scale and high dimensional single-cell data

aws cloud gene-expression gene-regulatory-network grpc large-scale-data-visualization loom reactjs single-cell

Last synced: 09 Apr 2025

https://github.com/xieguigang/mzkit

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

chemoinformatics gc-ms gcxgc kegg lc-ms lipidomics maldi mass-spectrometry metabolomics metadna ms-dial ms-imaging mzkit r-sharp raman-spectroscopy single-cell single-cell-metabolism visualbasic

Last synced: 19 Feb 2026

https://github.com/bioconductor/orchestratingsinglecellanalysis

Content for the OSCA Book.

book book-base rna-seq single-cell single-cell-rna-seq

Last synced: 17 Jun 2025

https://github.com/theislab/trvae

Conditional out-of-distribution prediction

cvae deep-learning generative-model mmd single-cell

Last synced: 11 Oct 2025

https://github.com/single-cell-genetics/cardelino

Clone identification from single-cell data

clonal-clustering gibbs-sampling scrna-seq single-cell somatic-mutations

Last synced: 21 Feb 2026

https://github.com/nathanskene/ewce

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

deconvolution single-cell single-cell-rna-seq transcriptomics

Last synced: 13 Apr 2025

https://github.com/earmingol/cell2cell

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

bioinformatics bulk-rna-seq cell-cell-communication cell-cell-interaction computational-biology machine-learning rna-seq rnaseq sc-rna-seq single-cell single-cell-rna-seq

Last synced: 14 Aug 2025

https://github.com/theislab/scib-reproducibility

Additional code and analysis from the single-cell integration benchmarking project

benchmarking integration results rna-seq scrna-seq single-cell website

Last synced: 11 Oct 2025

https://github.com/theislab/drvi

Unsupervised Deep Disentangled Representation of Single-Cell Omics

anndata bioinformatics disentanglement integration python single-cell transcriptomics

Last synced: 02 Mar 2026

https://baderlab.github.io/scClustViz/

Explore and share your scRNAseq clustering results

clustering-evaluation differential-expression r scrna-seq scrna-seq-analysis scrnaseq shiny single-cell ui

Last synced: 15 Nov 2025

https://github.com/immunogenomics/cna

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

python single-cell

Last synced: 07 May 2025

https://github.com/davisidarta/dbmap

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

denoising diffusion-process dimensionality-reduction graph-layout high-dimensional machine-learning nearest-neighbors single-cell umap visualization

Last synced: 06 Mar 2026

https://github.com/arc85/celltalker

Inference of cell-cell communication from single-cell RNAseq data

ligands receptors single-cell transcriptomics

Last synced: 30 Apr 2025

https://github.com/davisidarta/dbMAP

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

denoising diffusion-process dimensionality-reduction graph-layout high-dimensional machine-learning nearest-neighbors single-cell umap visualization